Lecture 3 - Making Proteins Lecture Notes PDF

Making proteins BIOL2020 Additional reading material: RNA polymerase: https://pdb101.rcsb.org/motm/40 Ribosome https://pdb101.rcsb.org/motm/121 Proteins are chains of amino acids with a 3d structure Primary structure = the amino acid sequence Secondary structure = Hydrogen bonds between amino ac...

Making proteins BIOL2020 Additional reading material: RNA polymerase: https://pdb101.rcsb.org/motm/40 Ribosome https://pdb101.rcsb.org/motm/121 Proteins are chains of amino acids with a 3d structure Primary structure = the amino acid sequence Secondary structure = Hydrogen bonds between amino acids form alpha helices or beta sheets Terciary structure = 3D structure of the protein A single polypeptide chain Quaternary structure = two or more polypeptides aka protiencomplex Nucleus The central dogma DNA → RNA → Protein Transcription: RNA polymerase uses DNA as a template to produce a pre-mRNA (transcript) Translation: A ribosome builds the protein molecule (polypeptide) from a mature mRNA. The protein is encoded in a gene. Cytoplasm The nucleus has two membranes (inner and outer) ● ● Chromatin: compact DNA Nucleolus encode ribosomal RNAs RNA Polymerase catalyzes the chemical reactions that synthesize RNA from a DNA template. DNA RNA RNA polymerase II Read: http://pdb101.rcsb.org/motm/40 There are many different types of RNA molecules and they serve different functions Three RNA polymerases • RNA polymerase I : rRNA genes, • RNA polymerase II : mRNA, miRNA, snRNA, and snoRNA genes • RNA polymerase III : tRNA and 5S rRNA genes. mRNAs messenger RNAs, code for proteins rRNAs ribosomal RNAs, form basic structure of ribosome; catalyze protein synthesis tRNAs transfer RNAs, adaptors between mRNA and amino acids snRNAs small nuclear RNAs, function in nuclear processes, The active site of RNA polymerase has two DNA stands and an RNA strand 1. 2. 3. Two DNA strands form a double helix at the top RNA polymerase separates the two DNA strands in the middle and builds an RNA strand the two DNA strands come back together See the structure in 3D https://www.rcsb.org/structure/1msw RNA pol recognizes the TATAAA box to initiate transcription • • • RNA pol II bind to TATA binding proteins TFIID starts the process of transcription, it recruits additional transcription factors. constructing a large protein complex TATA box is at the promoter (DNA region) TATA binding protein RNA pol DNA TATA Examples mRNA leaves the nucleus through the Nuclear Pore Complex Matteo Allegretti et al 2020 Nature • • • Particle movement by the NPC is controlled mRNA, ribosomes, and proteins leave the nucleus through the npc Protein import also happens through the npc Explore the structure of RNA polymerase. Find the DNA, RNA, and protein molecules https://www.rcsb.org/3d-view/1MSW/1 The ribosome read mRNA and translates the information into a polypeptide • • • The two subunits lock together with a mRNA trapped inside The ribosome then walks down the messenger RNA and translates the nucleotides into amino acid chains Three nucleotides (codon) = one amino acid The Ribosome is composed of a large catalytic subunit and a small subunit Large subunit Catalytic site (RNA) Contains the active site of the ribosome: the site that creates the new peptide bonds when proteins are synthesized. Finds a messenger RNA strand and ensures that each codon pairs with the anticodon Small subunit RNA molecules: orange and yellow The large subunit contains the active site of the ribosome: the site that creates the new peptide bonds Finds a messenger RNA strand and ensures that each codon pairs with the anticodon Large subunit Catalytic site (RNA) RNA molecules: orange and yellow The small subunit finds a messenger RNA strand and ensures that each codon pairs with the anticodon Contains the active site of the ribosome: the site that creates the new peptide bonds when proteins are synthesized. Small subunit RNA molecules: orange and yellow Transfer RNA (tRNA) translate the mRNA into amino acids • • tRNA serves as a link between the mRNA molecule and the growing chain of amino acids. Anticodons and codons The ribosome read mRNA and translates the information into a polypeptide • • • The two subunits lock together with a mRNA trapped inside The ribosome then walks down the messenger RNA and translates the nucleotides into amino acid chains Three nucleotides (codon) = one amino acids The start codon is the first codon of a mRNA transcript translated by a ribosome. Stop codon signals the termination of the translation process • • • • Start codon = methionine Stop codon = no aa There is no stop tRNA but a protein that stops translation (translation termination factor) Discuss: Why do cells need a nucleus? • • • Bacteria don’t have nucleus Bacteria make proteins faster than eukaryotes Moving mRNA out of the cytoplasm is complex and energy-demanding RNA splicing removes untranslated regions from mRNA • • • • • Splicing is common in eukaryotes Exons are that part of the RNA that code for proteins Introns are regions that resides within a gene but does not remain in the final mature mRNA Splicing happens in the nucleus Mature mRNA is exported by the nuclear pore complex Spliceosomes cut up the exons and reconnect them to produce the mRNA molecules that are used to make proteins. Additional information: https://pdb101.rcsb.org/motm/245 Splicing allows multiple proteins to be encoded in a single gene https://www.nature.com/scitable/topicpage/rna-splicing-introns-exons-and-spliceosome-12375/ Summary Transcription • Nucleus • DNA to mRNA • RNA polymerase Translation • Cytoplasm • mRNA to protein • Ribosome • tRNA Nuclear pore • connection between nucleus and cytoplasm Nucleus • Prevents Ribosome from translated unspliced mRNA • Two membranes